Pääbo's genetic bombshell seemed to confirm that Neanderthals were a separate species—but it does nothing to solve the mystery of why they vanished, and our species survived.

One obvious possibility is that modern humans were simply more clever, more sophisticated, more "human." Until recently, archaeologists pointed to a "great leap forward" around 40,000 years ago in Europe, when the Neanderthals' relatively humdrum stone tool industry—called Mousterian, after the site of Le Moustier in southwestern France—gave way to the more varied stone and bone tool kits, body ornaments, and other signs of symbolic expression associated with the appearance of modern humans. Some scientists, such as Stanford University anthropologist Richard Klein, still argue for some dramatic genetic change in the brain—possibly associated with a development in language—that propelled early modern humans to cultural dominance at the expense of their beetle-browed forebears.

But the evidence in the ground is not so cut and dried. In 1979 archaeologists discovered a late Neanderthal skeleton at Saint-Césaire in southwestern France surrounded not with typical Mousterian implements, but with a surprisingly modern repertoire of tools. In 1996 Jean-Jacques Hublin of the Max Planck Institute in Leipzig and Fred Spoor of University College London identified a Neanderthal bone in another French cave, near Arcy-sur-Cure, in a layer of sediment also containing ornamental objects previously associated only with modern humans, such as pierced animal teeth and ivory rings. Some scientists, such as British paleoanthropologist Paul Mellars, dismiss such modern "accessorizing" of a fundamentally archaic lifestyle as an "improbable coincidence"—a last gasp of imitative behavior by Neanderthals before the inventive newcomers out of Africa replaced them. But more recently, Francesco d'Errico of the University of Bordeaux and Marie Soressi, also at the Max Planck Institute in Leipzig, analyzed hundreds of crayon-like blocks of manganese dioxide from a French cave called Pech de l'Azé, where Neanderthals lived well before modern humans arrived in Europe. D'Errico and Soressi argue that the Neanderthals used the black pigment for body decoration, demonstrating that they were fully capable of achieving "behavioral modernity" all on their own.

"At the time of the biological transition," says Erik Trinkaus, a paleoanthropologist at Washington University in St. Louis, "the basic behavior [of the two groups] is pretty much the same, and any differences are likely to have been subtle." Trinkaus believes they indeed may have mated occasionally. He sees evidence of admixture between Neanderthals and modern humans in certain fossils, such as a 24,500-year-old skeleton of a young child discovered at the Portuguese site of Lagar Velho, and a 32,000-year-old skull from a cave called Muierii in Romania. "There were very few people on the landscape, and you need to find a mate and reproduce," says Trinkaus. "Why not? Humans are not known to be choosy. Sex happens."

It may have happened, other researchers say, but not often, and not in a way that left behind any evidence. Katerina Harvati, another researcher at the Max Planck Institute in Leipzig, has used detailed 3-D measurements of Neanderthal and early modern human fossils to predict exactly what hybrids between the two would have looked like. None of the fossils examined so far matches her predictions.